Filipe Jorge Garrett Vieira
Research Consultant
- 2023
- Published
Uncovering neutral and adaptive genomic differentiation among European perch with brackish water and freshwater origin in the western Baltic Sea region
Skovrind, Mikkel, Antunes Pacheco, George, Christensen, E. A. F., Gopalakrishnan, Shyam, Fietz, K., Holm-Hansen, T. H., Vieira, Filipe Garrett, Krag, M. A., Carl, Henrik, Gilbert, M Thomas P, Olsen, Morten Tange & Møller, Peter Rask, 2023, In: Fisheries Research. 268, 11 p., 106846.Research output: Contribution to journal › Journal article › Research › peer-review
- 2022
- Published
Intestinal metaplasia is a precursor lesion for sinonasal intestinal-type adenocarcinoma: genomic investigation of a case proving this hypothesis
Sjöstedt, S., Schmidt, A. Y., Vieira, Filipe Garrett, Woller, N. C., Nielsen, Finn Cilius & von Buchwald, Christian, Jan 2022, In: APMIS. 130, 1, p. 53-56 4 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Differences in gene expression despite identical histomorphology in sinonasal intestinal-type adenocarcinoma and metastases from colorectal adenocarcinoma
Sjöstedt, S., Vieira, Filipe Garrett, Karnov, K., Agander, T. K., Willemoe, G. L., Rohrberg, K. S., Nielsen, Finn Cilius & von Buchwald, Christian, 2022, In: APMIS. 130, 9, p. 551-559Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Origin and expansion of the world’s most widespread pinniped: Range-wide population genomics of the harbour seal (Phoca vitulina)
Liu, X., Schjøtt, S. R., Granquist, S. M., Rosing-Asvid, A., Dietz, R., Teilmann, J., Galatius, A., Cammen, K., O’Corry-Crowe, G., Harding, K., Härkönen, T., Hall, A., Carroll, E. L., Kobayashi, Y., Hammill, M., Stenson, G., Kirstine Frie, A., Lydersen, C., Kovacs, K. M., Andersen, L. W. & 6 others, , 2022, In: Molecular Ecology. 31, 6, p. 1682-1699Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade
Brandt, Luise Ørsted, Taurozzi, Alberto John, Mackie, Meaghan, Sinding, Mikkel Holger Strander, Vieira, Filipe Garrett, Schmidt, A. L., Rimstad, C., Collins, Matthew James & Mannering, U., 2022, In: PLoS ONE. 17, 7, 14 p., e0270040.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The population genomic legacy of the second plague pandemic
Gopalakrishnan, S., Ebenesersdóttir, S. S., Lundstrøm, I. K. C., Turner-Walker, G., Moore, K. H. S., Luisi, P., Margaryan, A., Martin, M. D., Ellegaard, M. R., Magnússon, Ó., Sigurðsson, Á., Snorradóttir, S., Magnúsdóttir, D. N., Laffoon, J. E., van Dorp, L., Liu, X., Moltke, I., Ávila-Arcos, M. C., Schraiber, J. G., Rasmussen, S. & 40 others, , 2022, In: Current Biology. 32, 21, p. 4743-4751.e6Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes
Iwanycki Ahlstrand, N., Gopalakrishnan, S., Vieira, F. G., Bieker, V. C., Meudt, H. M., Dunbar-Co, S., Rothfels, C. J., Martinez-Swatson, K. A., Maldonado, C., Hassemer, G., Shipunov, A., Bowers, M. D., Gardner, E., Xu, M., Ghorbani, A., Amano, M., Grace, O. M., Pringle, J. S., Bishop, M., Manzanilla, V. & 18 others, , 2022, In: Frontiers in Plant Science. 13, 16 p., 838166.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Viral and Genomic Drivers of Squamous Cell Neoplasms Arising in the Lacrimal Drainage System
Ramberg, Ingvild Margrethe Sellæg, Vieira, Filipe Garrett, Toft, Peter Bjerre, von Buchwald, Christian & Heegaard, Steffen, 2022, In: Cancers. 14, 10, 2558.Research output: Contribution to journal › Journal article › Research › peer-review
- 2021
- Published
Major driver mutations are shared between sinonasal intestinal-type adenocarcinoma and the morphologically identical colorectal adenocarcinoma
Sjöstedt, S., Schmidt, A. Y., Vieira, Filipe Garrett, Willemoe, G. L., Agander, T. K., Olsen, C., Nielsen, Finn Cilius & von Buchwald, Christian, Apr 2021, In: Journal of Cancer Research and Clinical Oncology. 147, 4, p. 1019-1027 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data
Gabrielaite, M., Torp, M., Rasmussen, M., Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C., Kinalis, S., Madsen, M., Yde, C., Rønn, O. L., Marvig, R., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, bioRxiv, 29 p.Research output: Working paper › Preprint › Research
- Published
A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data
Gabrielaite, M., Torp, M. H., Rasmussen, Malthe Sebro, Andreu-Sánchez, S., Vieira, Filipe Garrett, Pedersen, C. B., Kinalis, S., Madsen, M. B., Kodama, M., Demircan, G. S., Simonyan, A., Yde, C. W., Olsen, L. R., Marvig, R. L., Østrup, O., Rossing, Caroline Maria, Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2021, In: Cancers. 13, 24, 6283.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives: [version 2; peer review: 2 approved]
Westbury, Michael Vincent, Barnett, R., Sandoval-Velasco, Marcela, Gower, Graham, Vieira, Filipe Garrett, de Manuel, M., Hansen, Anders Johannes, Yamaguchi, N., Werdelin, L., Marques-Bonet, T., Gilbert, M Thomas P & Lorenzen, Eline, 2021, In: Open Research Europe. 1, 16 p., 25.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives: [version 1; peer review: 2 approved]
Westbury, Michael Vincent, Barnett, R., Sandoval-Velasco, Marcela, Gower, Graham, Vieira, Filipe Garrett, de Manuel, M., Hansen, Anders Johannes, Yamaguchi, N., Werdelin, L., Marques-Bonet, T., Gilbert, M Thomas P & Lorenzen, Eline, 2021, In: Open Research Europe. 1, 15 p., 25.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities
Piñeiro, R., Hardy, O. J., Tovar, C., Gopalakrishnan, Shyam, Vieira, Filipe Garrett & Gilbert, M Thomas P, 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 27, 9 p., e2013979118.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic alterations in human papillomavirus-positive and -negative conjunctival squamous cell carcinomas
Ramberg, Ingvild Margrethe Sellæg, Vieira, Filipe Garrett, Toft, Peter Bjerre, von Buchwald, Christian, Funding, M., Nielsen, Finn Cilius & Heegaard, Steffen, 2021, In: Investigative Ophthalmology and Visual Science. 62, 14, 11.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Germline RET Leu56Met Variant Is Likely Not Causative of Multiple Endocrine Neoplasia Type 2
Hansen, A. R., Borgwardt, L., Rasmussen, Å. K., Godballe, C., Poulsen, M. M., Vieira, Filipe Garrett, Mathiesen, J. S. & Rossing, Caroline Maria, 2021, In: Frontiers in Endocrinology. 12, 764512.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)
Sánchez-Barreiro, F., Gopalakrishnan, Shyam, Ramos Madrigal, Jazmin, Westbury, Michael Vincent, de Manuel, M., Margaryan, Ashot, Ciucani, M. M., Vieira, Filipe Garrett, Patramanis, Ioannis, Kalthoff, D. C., Timmons, Z., Sicheritz-Pontén, Thomas, Dalén, L., Ryder, O. A., KU, thw266, Marques-Bonet, T., Moodley, Y. & Gilbert, M Thomas P, 2021, In: Molecular Ecology. 30, 23, p. 6355-6369 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos
Sinding, M. S., Ciucani, M. M., Ramos Madrigal, Jazmin, Carmagnini, A., Rasmussen, Jacob Agerbo, Feng, S., Chen, G., Vieira, Filipe Garrett, Mattiangeli, V., Ganjoo, R. K., Larson, G., Sicheritz-Pontén, Thomas, Petersen, Bent, Frantz, L., Gilbert, M Thomas P & Bradley, D. G., 2021, In: iScience. 24, 11, 18 p., 103226.Research output: Contribution to journal › Journal article › Research › peer-review
- 2020
- Published
Arctic-adapted dogs emerged at the Pleistocene-Holocene transition
Sinding, M. H. S., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Pitulko, V. V., Kuderna, L., Feuerborn, T. R., Frantz, L. A. F., Vieira, F. G., Niemann, J., Samaniego Castruita, J. A., Carøe, C., Andersen-Ranberg, E. U., Jordan, P. D., Pavlova, E. Y., Nikolskiy, P. A., Kasparov, A. K., Ivanova, V. V., Willerslev, E., Skoglund, P. & 15 others, , 2020, In: Science (New York, N.Y.). 368, 6498, p. 1495-1499 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Conservation genetics of the critically endangered Siamese rosewood (Dalbergia cochinchinensis): recommendations for management and sustainable use
Hartvig, Ida, So, T., Changtragoon, S., Tran, H. T., Bouamanivong, S., Ogden, R., Senn, H., Vieira, Filipe Garrett, Turner, F., Talbot, R., Theilade, Ida, Nielsen, Lene Rostgaard & Kjær, Erik Dahl, 2020, In: Conservation Genetics. 21, p. 677-692Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds
Antunes Pacheco, George, van Grouw, H., Shapiro, M. D., Gilbert, M Thomas P & Vieira, Filipe Garrett, 2020, In: Genome Biology and Evolution. 12, 3, p. 136-150 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens
Barnett, R., Westbury, M. V., Sandoval-Velasco, M., Vieira, F. G., Jeon, S., Zazula, G., Martin, M. D., Ho, S. Y. W., Mather, N., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Zepeda-Mendoza, M. L., Antunes, A., Baez, A. C., De Cahsan, B., Larson, G., O’Brien, S. J., Eizirik, E., Johnson, W. E. & 11 others, , 2020, In: Current Biology. 30, p. 5018-5025Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros
Margaryan, Ashot, Sinding, Mikkel Holger Strander, Liu, Shanlin, Vieira, Filipe Garrett, Chan, Y. L., Nathan, S. K. S. S., Moodley, Y., Bruford, M. W. & Gilbert, M Thomas P, 2020, In: Zoological Journal of the Linnean Society. 190, 1, p. 372-383 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The evolutionary history of extinct and living lions
de Manuel, M., Barnett, R., Sandoval-Velasco, M., Yamaguchi, N., Vieira, F. G., Mendoza, M. L. Z., Liu, S., Martin, M. D., Sinding, M-H. S., Mak, S. S. T., Caroe, C., Liu, S., Guo, C., Zheng, J., Zazula, G., Baryshnikov, G., Eizirik, E., Koepfli, K-P., Johnson, W. E., Antunes, A. & 9 others, , 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 20, p. 10927-10934 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction
Vieira, Filipe Garrett, Castruita, J. A. S. & Gilbert, M Thomas P, 2020, In: Ecology and Evolution. 10, 23, p. 12700-12709Research output: Contribution to journal › Journal article › Research › peer-review
- 2019
- Published
ngsLD: evaluating linkage disequilibrium using genotype likelihoods
Fox, E. A., Wright, A. E., Fumagalli, M. & Vieira, Filipe Garrett, 1 Oct 2019, In: Bioinformatics (Oxford, England). 35, 19, p. 3855-3856 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
- Published
Parallel adaptation of rabbit populations to myxoma virus
Alves, J. M., Carneiro, M., Cheng, J. Y., Matos, A. L. D., Rahman, M. M., Loog, L., Campos, P. F., Wales, N., Eriksson, A., Manica, A., Strive, T., Graham, S. C., Afonso, S., Bell, D. J., Belmont, L., Day, J. P., Fuller, S. J., Marchandeau, S., Palmer, W. J., Queney, G. & 8 others, , 2019, In: Science. 363, 6433Research output: Contribution to journal › Journal article › Research › peer-review
- 2018
- Published
Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull
Bro-Jørgensen, M. H., Carøe, C., Vieira, Filipe Garrett, Nestor, S., Hallström, A., Gregersen, K. M., Etting, V., Gilbert, M Thomas P & Sinding, Mikkel Holger Strander, 1 Nov 2018, In: Journal of Archaeological Science. 99, p. 47-54 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture
Wright, A. E., Fumagalli, M., Cooney, C. R., Bloch, N. I., Vieira, Filipe Garrett, Buechel, S. D., Kolm, N. & Mank, J. E., Apr 2018, In: Evolution Letters. 2, 2, p. 52-61 10 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines
Hernandez, Y., Bernstein, R., Pagan, P., Vargas, L., McCaig, W., Ramrattan, G., Akther, S., Larracuente, A., Di, L., Vieira, Filipe Garrett & Qiu, W., 2 Mar 2018, In: B M C Bioinformatics. 19, 7 p., 76.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq
Kodama, M., Brinch-pedersen, H., Sharma, S., Holme, I. B., Joernsgaard, B., Dzhanfezova, T., Amby, Daniel Buchvaldt, Vieira, Filipe Garrett, Liu, Shanlin & Gilbert, M. T. P., 2018, In: BMC Genomics. 19, 13 p., 811.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Interspecific Gene Flow Shaped the Evolution of the Genus Canis
Gopalakrishnan, S., Sinding, M. H. S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J. A., Vieira, F. G., Carøe, C., Montero, M. D. M., Kuderna, L., Serres, A., González-Basallote, V. M., Liu, Y. H., Wang, G. D., Marques-Bonet, T., Mirarab, S., Fernandes, C., Gaubert, P., Koepfli, K. P., Budd, J., Rueness, E. K. & 7 others, , 2018, In: Current Biology. 28, 21, p. 3441-3449Research output: Contribution to journal › Journal article › Research › peer-review
- Published
No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon
Barnett, R., Sinding, M. S., Vieira, Filipe Garrett, Mendoza, M. L. Z., Bonnet, M., Araldi, A., Kienast, I., Zambarda, A., Yamaguchi, N., Henschel, P. & Gilbert, M Thomas P, 2018, In: Conservation Genetics. 19, 3, p. 611-618 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Population genomics of grey wolves and wolf-like canids in North America
Sinding, Mikkel Holger Strander, Gopalakrishan, S., Vieira, Filipe Garrett, Samaniego Castruita, J. A., Raundrup, K., Heide-Jørgensen, M. P., Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, T., Mikkelsen, J. B., Marquard-Petersen, U., Dietz, R., Sonne, C., Dalén, L., Bachmann, L., Wiig, Ø., Hansen, Anders Johannes & Gilbert, M Thomas P, 2018, In: PLOS Genetics. 14, 11, 23 p., e1007745.Research output: Contribution to journal › Journal article › Research › peer-review
- 2017
- Published
Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes
Biard, V., Gol'din, P., Gladilina, E., Vishnyakova, K., McGrath, K., Vieira, Filipe Garrett, Wales, N., Fontaine, M. C., Speller, C. & Olsen, Morten Tange, Oct 2017, In: Journal of Archaeological Science: Reports. 15, p. 262-271 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Unmatched DNA preservation prove arctic hare and sheep wool in Norse Greenlandic textile from “The Farm Beneath the Sand”
Sinding, Mikkel Holger Strander, Vieira, Filipe Garrett & Smith, M. H., 1 Aug 2017, In: Journal of Archaeological Science: Reports. 14, p. 603-608 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, C., Geng, C., Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, Filipe Garrett, Germonpré, M., Bocherens, H., Fedorov, S., Petersen, Bent, Sicheritz-Pontén, T., Marques-Bonet, T., KU, thw266, Jiang, H. & Gilbert, M Thomas P, Aug 2017, In: GigaScience. 6, 8, p. 1–13 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
Wang, H., Vieira, Filipe Garrett, Crawford, J. E., Chu, C. & Nielsen, R., Jun 2017, In: Genome Research. 27, 6, p. 1029-1038 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes
Sanchez Barreiro, F., Vieira, Filipe Garrett, Martin, M. D., Haile, James Seymour, Gilbert, M Thomas P & Wales, N., 2017, In: Molecular Ecology Resources. 17, 2, p. 209-220 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
The power of inbreeding: NGS-based GWAS of rice reveals convergent evolution during rice domestication
Wang, H., Xu, X., Vieira, Filipe Garrett, Xiao, Y., Li, Z., Wang, J., Nielsen, Rasmus & Chu, C., 6 Jul 2016, In: Molecular Plant. 9, 7, p. 975-985 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
Foote, A. D., Vijay, N., Avila Arcos, M. D. C., Baird, R. W., Durban, J. W., Fumagalli, M., Gibbs, R. A., Hanson, M. B., Korneliussen, Thorfinn Sand, Martin, M. D., Robertson, K. M., Sousa, V. C., Vieira, Filipe Garrett, Vinař, T., Wade, P., Worley, K. C., Excoffier, L., Morin, P. A., Gilbert, M Thomas P & Wolf, J. B. W., May 2016, In: Nature Communications. 7, 12 p., 11693.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating IBD tracts from low coverage NGS data
Vieira, Filipe Garrett, Albrechtsen, Anders & Nielsen, Rasmus, 2016, In: Bioinformatics. 32, 14, p. 2096-2102 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans
Martin, M. D., Vieira, Filipe Garrett, Ho, S. Y. W., Wales, N., Schubert, Mikkel, Seguin-Orlando, A., Ristaino, J. B. & Gilbert, M Thomas P, 2016, In: Molecular Biology and Evolution. 33, 2, p. 478-491 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic insights into the Ixodes scapularis tick vector of Lyme disease
Gulia-Nuss, M., Nuss, A. B., Meyer, J. M., Sonenshine, D. E., Roe, R. M., Waterhouse, R. M., Sattelle, D. B., de la Fuente, J., Ribeiro, J. M., Megy, K., Thimmapuram, J., Miller, J. R., Walenz, B. P., Koren, S., Hostetler, J. B., Thiagarajan, M., Joardar, V. S., Hannick, L. I., Bidwell, S., Hammond, M. P. & 73 others, , 2016, In: Nature Communications. 7, 13 p., 10507.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe
Skovrind, Mikkel, Olsen, Morten Tange, Vieira, Filipe Garrett, Antunes Pacheco, George, Carl, Henrik, Gilbert, M Thomas P & Møller, Peter Rask, 2016, In: Ecology and Evolution. 6, 4, p. 1064-1074 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Improving the estimation of genetic distances from Next-Generation Sequencing data
Vieira, Filipe Garrett, Lassalle, F., Korneliussen, Thorfinn Sand & Fumagalli, M., 2016, In: Biological Journal of the Linnean Society. 117, 1, p. 139-149 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2015
- Published
Evolutionary genomics and conservation of the endangered Przewalski's horse
Der Sarkissian, C., Ermini, L., Schubert, M., Yang, M. A., Sanz, P. L., Fumagalli, M., Jónsson, H., Bar-Gal, G. K., Albrechtsen, A., Garrett Vieira, F. J., Petersen, B., Ginolhac, A., Seguin-Orlando, A., Magnussen, K., Fages, A. A., Gamba, C., Lorente-Galdos, B., Polani, S., Steiner, C., Neuditschko, M. & 17 others, , 2015, In: Current Biology. 25, 19, p. 2577-2583 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The origin and evolution of maize in the Southwestern United States: [+ erratum]
Rodrigues da Fonseca, Rute Andreia, Smith, B. D., Wales, N., Cappellini, Enrico, Skoglund, P., Fumagalli, M., Samaniego Castruita, J. A., Carøe, C., Avila Arcos, M. D. C., Hufnagel, D. E., Korneliussen, Thorfinn Sand, Vieira, Filipe Garrett, Jakobsson, M., Arriaza, B., Willerslev, Eske, Nielsen, Rasmus, Hufford, M. B., Albrechtsen, Anders, Ross-Ibarra, J. & Gilbert, M Thomas P, 2015, In: Nature Plants. 1, 5 p., 14003.Research output: Contribution to journal › Letter › Research › peer-review
- 2014
Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families
Librado, P., Vieira, Filipe Garrett, Sánchez-Gracia, A., Kolokotronis, S. O. & Rozas, J., Jun 2014, In: Genome Biology and Evolution. 6, 6, p. 1454-1465 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
ngsTools : methods for population genetics analyses from next-generation sequencing data
Fumagalli, M., Vieira, Filipe Garrett, Linderoth, T. & Nielsen, Rasmus, 2014, In: Bioinformatics. 30, 10, p. 1486-1487 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2013
- Published
Quantifying population genetic differentiation from next-generation sequencing data
Fumagalli, M., Vieira, Filipe Garrett, Korneliussen, Thorfinn Sand, Linderoth, T., Huerta-Sánchez, E., Albrechtsen, Anders & Nielsen, Rasmus, Nov 2013, In: Genetics. 195, 3, p. 979-992 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
Vieira, Filipe Garrett, Fumagalli, M., Albrechtsen, Anders & Nielsen, Rasmus, 2013, In: Genome Research. 23, p. 1852-1861 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2012
Unique features of odorant-binding proteins of the parasitoid wasp Nasonia vitripennis revealed by genome annotation and comparative analyses
Vieira, Filipe Garrett, Forêt, S., He, X., Rozas, J., Field, L. M. & Zhou, J. J., 27 Aug 2012, In: PLoS ONE. 7, 8, e43034.Research output: Contribution to journal › Journal article › Research › peer-review
BadiRate: Estimating family turnover rates by likelihood-based methods
Librado, P., Vieira, Filipe Garrett & Rozas, J., Jan 2012, In: Bioinformatics. 28, 2, p. 279-281 3 p., btr623.Research output: Contribution to journal › Journal article › Research › peer-review
- 2011
Comparative Genomics of the Major Chemosensory Gene Families in Arthropods
Sánchez-Gracia, A., Vieira, Filipe Garrett, Almeida, F. C. & Rozas, J., 2011, Encyclopedia of Life Sciences. WileyResearch output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
Comparative genomics of the odorant-binding and chemosensory protein gene families across the arthropoda: Origin and evolutionary history of the chemosensory system
Vieira, Filipe Garrett & Rozas, J., 2011, In: Genome Biology and Evolution. 3, 1, p. 476-490 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2010
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
Kirkness, E. F., Haas, B. J., Sun, W., Braig, H. R., Perotti, M. A., Clark, J. M., Lee, S. H., Robertson, H. M., Kennedy, R. C., Elhaik, E., Gerlach, D., Kriventseva, E. V., Elsik, C. G., Graur, D., Hill, C. A., Veenstra, J. A., Walenz, B., Tubío, J. M. C., Ribeiro, J. M. C., Rozas, J. & 51 others, , 6 Jul 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 27, p. 12168-12173 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum
Zhou, J. J., Vieira, Filipe Garrett, He, X. L., Smadja, C., Liu, R., Rozas, J. & Field, L. M., Mar 2010, In: Insect Molecular Biology. 19, SUPPL. 2, p. 113-122 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
Genome sequence of the pea aphid Acyrthosiphon pisum
Richards, S., Gibbs, R. A., Gerardo, N. M., Moran, N., Nakabachi, A., Stern, D., Tagu, D., Wilson, A. C. C., Muzny, D., Kovar, C., Cree, A., Chacko, J., Chandrabose, M. N., Dao, M. D., Dinh, H. H., Gabisi, R. A., Hines, S., Hume, J., Jhangian, S. N., Joshi, V. & 200 others, , 2010, In: PLoS Biology. 8, 2, e1000313.Research output: Contribution to journal › Journal article › Research › peer-review
- 2009
Molecular evolution of the major chemosensory gene families in insects
Sánchez-Gracia, A., Vieira, Filipe Garrett & Rozas, J., Sep 2009, In: Heredity. 103, 3, p. 208-216 9 p.Research output: Contribution to journal › Review › Research › peer-review
- 2008
Processing of a membrane protein required for cell-to-cell signaling during endospore formation in Bacillus subtilis
Serrano, M., Vieira, Filipe Garrett, Moran, C. P. & Henriques, A. O., Dec 2008, In: Journal of Bacteriology. 190, 23, p. 7786-7796 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- 2007
Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: Purifying selection and birth-and-death evolution
Vieira, Filipe Garrett, Sánchez-Gracia, A. & Rozas, J., 8 Nov 2007, In: Genome Biology (Online). 8, 11, R235.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Evolution of genes and genomes on the Drosophila phylogeny. Drosophila 12 Genomes Consortium
Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W. & 31 others, , 2007, In: Nature. 450, 7167, p. 203-18 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
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Genomic insights into the Ixodes scapularis tick vector of Lyme disease
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Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
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